Former Members

 

BIOSYSTEMS ENGINEERING RESEARCH GROUP 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

Ph.D.

  • Ceyda Kasavi, Ph.D., 2013

Thesis: A System Based Rational Approach to Improve First and Second Generation Bioethanol Production by Saccharomyces cerevisiae 

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Assoc. Prof. Dr. Ebru Toksoy Öner

  • Ayça Cankorur Çetinkaya, Ph.D., 2013

Thesis: A System Based Approach to Understand Human Disorders Using Saccharomyces cerevisiae as a Model Organism 

Advisor: Prof. Dr. Betül Kırdar

  • Elif Dereli, Ph.D., 2013

Thesis: An Integrated Approach to Investigate TOR Signaling Mechanism in Saccharomyces cerevisiae 

Advisor: Prof. Dr. Betül Kırdar

  • Esra Börklü Yücel, Ph.D., 2013

Thesis: Investigation of Aging (Chronological Life Span) in S. cerevisiae by Systems Biology Approaches

Advisor: Prof. Dr. Kutlu Ülgen

  • Saliha Durmuş Tekir, Ph.D., 2013

Thesis: Investigation of Infection Mechanisms through Pathogen-Human Protein-Protein Interactions by Bioinformatics Approaches 

Advisor: Prof. Dr. Kutlu Ülgen

  • Duygu Dikicioğlu, Ph.D., 2011

Thesis: Investigation of the Effect of Plasticity on the Prediction of Genetic Interactions and Phenotypes in Saccharomyces cerevisiae 

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Stephen G. Oliver

  • Senem Tiveci, Ph.D., 2011

Thesis: Calcium Signaling System in Multiple Species: Structural and Functional Analyses of Protein Interaction Networks

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Prof. Dr. Türkan Haliloğlu

  • F. Betül Kavun Özbayraktar, Ph.D., 2011

Thesis: From Yeast to Human: Unraveling Sphingolipid Metabolism through Macroscopic and Microscopic Analyses 

Advisor: Prof. Dr. Kutlu Ülgen

  • Deniz Rende, Ph.D., 2010

Thesis: Development of a Systems Based Modular Approach to Link Complex Diseases

Advisor: Prof. Dr. Betül Kırdar

  • Kazım Yalçın Arga, Ph.D., 2007

Thesis: Analysis of Glucose Signaling Network in S. cerevisiae by Systems Biology Approach

Advisor: Prof. Dr. Kutlu Ülgen

  • Tunahan Çakır, Ph.D., 2006

Thesis: Integration of ‘Omics’ Data into Metabolic Stoichiometric Models

Advisor: Prof. Dr. Kutlu Ülgen 

  • Pınar Pir, Ph.D., 2005

Thesis: Integrated analysis of metabolome-transcriptome profiles in respiratory deficient deletion mutants in yeast

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Prof. Dr. Zeynep İlsen Önsan 

  • A.Tunga Akarsubaşı, Ph.D., 2003

Thesis: Characterization of methane bacteria in anaerobic treatment using 16S rDNA analysis

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Assoc.Prof.Dr. Bahar İnce 

  • Mehmet Mete Altıntaş, Ph.D., 2001

Thesis: Bioreactor Operating Strategies for Alcohol Fermentation by Recombinant Yeast

Advisor: Prof. Dr. Kutlu Ülgen 

  • Ebru Toksoy, Ph.D., 2000

Thesis: Production of TaqI Restriction and Modification Enzymes by using Two Different Expression Systems

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Serpil Ünlü, Ph.D, 1998

Thesis: Identification of Point Mutations and Improvement of Deletion Carriers in Turkish DMD/BMD Families

Advisor: Prof. Dr. Betül Kırdar 

  • Gülnur Birol, Ph.D,1997

Thesis: Studies on the Fermentation Characteristics of the Genetically Engineered Saccharomyces cerevisae

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan

  • Candan (Tamerler) Yıldır ,Ph.D,1996

Thesis: Studies on the Development of Chromatographic Methods for the Purification of Restriction Endonucleases

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

 

M.Sc. 

  • Gizem Özbüyükkaya, M.Sc., 2012

Thesis: Prediction of Potential Inhibitors against Yersinia YopE and Salmonella SopE by Virtual Screening and Docking

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Assist. Prof. Elif Özkırımlı

  • Deniz Menekşedağ, M.Sc., 2012

Thesis: Beta-Lactamase Ligand Recognition

Advisor: Assist. Prof. Elif Özkırımlı

Co-advisor: Assoc. Prof. Berna Sarıyar Akbulut

  • Begüm Alaybeyoğlu, M.Sc., 2012

Thesis: Understanding the Membrane Penetration of Antimicrobial Peptides

Advisor: Assist. Prof. Elif Özkırımlı

Co-advisor: Assoc. Prof. Berna Sarıyar Akbulut

  • Okan Yüzüak, M.Sc., 2012

Thesis: Functional Analysis of the Genes in the Glucose Metabolic Network by a System Based Modular Approach

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Assist. Prof. Elif Özkırımlı

  • Ahmet Özcan, M.Sc., 2011

Thesis: Effect of Protonation States of Catalytically Important Residues and Active Site Water Molecules on PTP1B Conformation

Advisor: Assist. Prof. Elif Özkırımlı Ölmez

Co-Advisor: Assist. Prof. Burak Alakent

  • Bahar Nalbantoğlu, M.Sc., 2011

Thesis: Investigation of Linear Paths in Human WNT Signaling Network

Advisor: Prof. Kutlu Ülgen

  • Celal Ceylan, M.Sc., 2010

Thesis: TEM-1 β-Lactamase Activity in the Presence of BLIP in Cellular Enviroments

Advisor: Assist. Prof. Elif Özkırımlı Ölmez

Co-Advisor: Assist. Prof. Berna Sarıyar Akbulut (Marmara University)

  • Ebru Demirci, M.Sc., 2010

Thesis: Identification of Key Transcription Factors in Glucose Sensing Pathway in Saccharomyces cerevisiae

Advisor: Prof. Dr. Betül Kırdar

  • Aysun Eren, M.Sc., 2010

Thesis: Investigation of Crosstalk Between WNT and HEDGEHOG Signaling Pathways

Advisor: Prof. Dr. Kutlu Ülgen

  • Yasemen Güngörmez, M.Sc., 2010

Thesis: Computational Prediction of Protein-Protein Interactions in Sphingolipid Signaling Network

Advisor: Prof. Dr. Kutlu Ülgen

Co-Advisor: Assist. Prof. Elif Özkırımlı Ölmez

  • Kübra Büyükyanbolu, M.Sc., 2010

Thesis: Investigation of the Relationship Between Sphingolipid and Insulin Signaling Pathways

Advisor: Prof. Dr. Kutlu Ülgen

  • Burcu Özkaral, M.Sc., 2010

Thesis: Investigation of PTP1B Activation Mechanism by Computational Methods

Advisor: Assist. Prof. Elif Özkırımlı

Co-Advisor: Assist. Prof. Burak Alakent

  • Ayşe Ezgi Akkaya, M.Sc., 2010

Thesis: Investigation of In-vivo Inhibition of β-lactamase by β-lactamase Inhibitor Protein

Advisor: Assist. Prof. Elif Özkırımlı

Co-Advisor: Assist. Prof. Berna Sarıyar Akbulut

  • Çiğdem Filiz, M.Sc., 2009

Thesis: Reconstruction of Cardiomyocyte Energy Metabolism and Investigation of the Healthy and Disease Cases by Metabolic Engineering Techniques

Advisor: Prof. Dr. Kutlu Ülgen

  • Pelin Ümit, M.Sc., 2009

Thesis: Reconstruction of Insulin Signaling Network in H.sapiens

Advisor: Prof. Dr. Kutlu Ülgen

  • Güray Kuzu, M.Sc., 2009

Thesis: Effect of Rapamycin and Caffeine on TOR Signaling Pathway in S.cerevisiae

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Assist. Prof. Elif Özkırımlı

  • Aylin Sanoviç, M.Sc., 2009

Thesis: Studies on the Genes Controlling Glucose Signaling in Yeast using Systems Dynamics

Advisor: Prof. Dr. Betül Kırdar  

  • Banu Yavuztürk, M.Sc., 2009

Thesis: Drug Target Identification by Investigating Sphingolipid Profiles in Yeast

Advisor: Prof. Dr. Kutlu Ülgen 

  • Feras Alazi, M.Sc., 2009

Thesis: Investigation of Noncanonical Wnt Signaling Network In C. Elegans

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Prof. Dr. Türkan Haliloğlu  

  • Pınar Kanlıkılıçer, M.Sc., 2009

Thesis: Investigation of beta-lactamase ligand binding in vivo and in silico

Advisor: Prof. Dr. Amable Hortaçsu

Co-advisor: Assist. Prof. Elif Özkırımlı 

  • Dicle Hasdemir, M.Sc., 2008

Thesis: Integration of interactome and transcriptome data to reveal glucose repression pathway in Saccharomyces cerevisiae

Advisor: Prof. Dr. Betül Kırdar 

  • Hilal Candan Karabıyık, M.Sc., 2008 

Thesis: in silico Determination of Protein Complexes in Yeast

Advisor: Prof. Dr. Betül Kırdar  

  • Nil Çınar, M.Sc., 2008

Thesis: Determination of Differentially Expressed Genes and Perturbation- Responsive Transcription Factors in Yeast

Advisor: Prof. Dr. Betül Kırdar  

  • Ece Acuner, M.Sc., 2008

Thesis: Structural Analysis of Mammalian Toll-like Receptor Signaling Network

Advisor: Prof. Dr. Kutlu Ülgen 

  • Enes Oruç, M.Sc., 2008

Thesis: Reconstruction of domain-domain interaction network of Wnt signaling in C. elegans

Advisor: Prof. Dr. Kutlu Ülgen 

  • Erdem Aygök, M.Sc., 2007

Thesis: Metabolite Footprinting and Fingerprinting in Yeast

Advisor: Prof. Dr. Kutlu Ülgen 

  • Can Çavlı, M.Sc., 2007

Thesis: Game Theoretical Analysis of Dynamic Glucose Signal Transduction Pathways in Saccharomyces Cerevisiae

Advisor: Prof. Dr. Kutlu Ülgen 

  • Selin Taşdöğen, M.Sc., 2007

Thesis: Integrated Neurovascular Coupling Model In Migraine Patients

Advisor: Prof. Dr. Kutlu Ülgen 

  • Burcu Öztürk, M.Sc.,2006     

Thesis: Experimental Studies for Optimal Production of  Cytoplasmic and periplasmic Thermostable Glucose Isomerase in Eschericiha coli

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Amable Hortaçsu 

  • Beste Kınıkoğlu, M.Sc., 2006

Thesis: Recostruction of Network Topology of Transgriptional Regulation in Yeast

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Hatice Kınış, M.Sc., 2005

Thesis: Experimental Investigation of Characteristics of some Glucose Transport Deficient Mutants in S. cerevisiae

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Prof. Dr. Zeynep İlsen Önsan 

  • Selma Alsan, M.Sc., 2005

Thesis: Modelling of Neurotransmitter Glutamate Via Metabolic Flux Analysis         

Advisor: Prof. Dr. Kutlu Ülgen 

  • Cüneyt Katıel, M.Sc., 2004

Thesis: Optimisation of Operating Conditions for the Purification of PstI Endonuclease

Advisor: Prof. Dr. Kutlu Ülgen 

  • Azra Köne, M.Sc., 2004

Thesis: Process Design and Economic Evaluation for the Production of Pharmaceuticals

Advisor: Prof. Dr. Kutlu Ülgen 

  • Serhan Tacer, M.Sc., 2004

Thesis: Enzymopathies- Extreme Pathway Analysis of Human Red Blood Cells

Advisor: Prof. Dr. Kutlu Ülgen 

  • Senem Tiveci, M.Sc., 2004

Thesis: The Role of Calcium Dynamics In Brain-Energy Metabolism

Advisor: Prof. Dr. Kutlu Ülgen 

  • I. Emrah Nikerel, M.Sc., 2003

Thesis: Statistical optimization of medium for the production of TaqI endonuclease from recombinant E.coli cells using response surface methodology

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Assis. Prof. Dr. Ramazan Yıldırım 

  • Hilal Taymaz, M.Sc., 2003

Thesis: Contribution of coagulation/fibrinolysis factors to the risk of ischemic cardiovascular disease: their genetic determinants

Advisor: Prof. Dr. Betül Kırdar             

  • Çağrı Efe, M.Sc., 2003

Thesis: Investigation of ethanol production by respiratory deficient industrial yeast strain

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Amable Hortaçsu 

  • Nigar Kantarcı, M.Sc., 2003

Thesis: Hydrodynamics and Heat Transfer Effects in a Bubble Column

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Prof. Dr. Fahir Borak 

  • Neslihan Günel, M.Sc., 2002

Thesis: Expression of recombinant CFTR protein by using two different expression systems

Advisor: Assoc. Prof. Kutlu Ülgen

Co-advisor: Prof. Dr. Betül Kırdar

  • Fatma Günel, M.Sc., 2002

Thesis: Bioprocess Design of a Therapeutic Protein

Advisor: Prof. Dr. Kutlu Ülgen

Co-advisor: Prof. Dr. Zeynep İlsen Önsan

  • Ayşe Sinem Özyurt, M.Sc., 2001

Thesis: Purification of Therapeutical Recombinant Proteins of Human Origin

Advisor: Assoc. Prof. Kutlu Ülgen

Co-advisor: Prof. Dr. Betül Kırdar

  • Erdem Çelik, M.Sc., 2001

Thesis: Purification of PstI Endonuclease from Providencia Stuartii 164

Advisor: Assoc. Prof. Kutlu Ülgen 

  • Osman Eksik, M.Sc., 2000

Thesis: Production of TaqI Endonuclease from Genetically Engineered E.coli BL21 (DE3) (pETaq(R +M))

Advisor: Prof. Dr. Betül Kırdar  

  • Bahar Bilgen, M.Sc., 2000

Thesis: Production of MBP-TaqI Restriction Endonuclease Fusion Protein by Recombinant e.coli Harbouring pETMET

Advisor: Prof. Dr. Betül Kırdar

  • Erdem Güzeltunç, M.Sc., 2000

Thesis: Development of Expanded Bed Technique for Purification of Actinorhodin from Streptomyces coelicolor A3(2)

Advisor: Assoc. Prof. Kutlu Ülgen 

  • Başak Elif Saygılı, M.Sc.,1999

Thesis: Single Step Conversion of Starch to Ethanol by Recombinant S.cerevisiae YPG/AB

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Nevra Özer, M.Sc., 1999

Thesis: A Study on Protein and DNA Analysis by Capillary Electrophoresis

Advisor: Assoc.Prof.Dr.Kutlu Ülgen

Co-advisor: Prof. Dr. Betül Kırdar  

  • Nedret Ümit, M.Sc., 1999

Thesis: Fuzzy Modeling and Control of a Biological Process

Advisor: Prof. Mehmet Çamurdan

Co-advisor: Assoc. Prof. Kutlu Ülgen 

  • Mehmet Gürcan Düzenli, M.Sc., 1999

Thesis: Modelling of the Purification of TaqI Endonuclease by Linear Gradient Elution Ion Exchange Chromatography

Advisor: Assoc. Prof. Kutlu Ülgen 

  • Fedai Akdeniz, M.Sc., 1999

Thesis: Modelling and Experimental Studies of Protein Purification in an Expanded Bed Adsorption Chromatography

Advisor: Assoc. Prof. Kutlu Ülgen 

  • Seda Savaş, M.Sc., 1998

Thesis: The Effect of Fermentation Conditions on a-Amylase and Glucoamylase production by a Recombinant Yeast strain

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Berna Sarıyar, M.Sc., 1997

Thesis: Production of Thermostable Thermus Thermophilus Glucose Isomerase in E.coli

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Amable Hortaçsu 

  • Alp Kırmaz, M.Sc., 1997

Thesis: Estimation of Biomass and Product Concentrations from Measured Substrate Concentration via Asymptotic Observer 

Advisor: Prof. Mehmet Çamurdan

Co-advisor: Assoc. Prof. Kutlu Ülgen 

  • Semra Yılmaz, M.Sc., 1997

Thesis: Optimization of Operating Parameters for Protein Purification with Chromatographic Columns

Advisor: Assoc. Prof. Kutlu Ülgen 

  • Z.Petek Çakar, M.Sc., 1996

Thesis: Cloning and expression of TaqI Endonuclease in E.coli by using the Cloning Vector pUC18

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Rana Türkkan, M.Sc., 1996

Thesis: Studies on the Development of a Small Scale Purification Procedure for PstI Endonuclease

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Mete Altıntaş, M.Sc., 1996

Thesis: Fermentation Characteristics of Thermus aquaticus and the Purification of its Enzyme TaqI

Advisor: Assoc. Prof. Kutlu Ülgen 

  • Ebru Toksoy, M.Sc., 1995

Thesis: Cloning and Purification of a Thermostable DNA Polymerase

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Elvan Solay, M.Sc., 1992

Thesis: Experimental Studies on Continious Ethanol Production by Immobilized Growing S.cerevisiae

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Gülnur Birol, M.Sc., 1992

Thesis: Cell Growth and Ethanol Production Characteristics of Immobilized S.cerevisiae in a Batch System with Nutrient Recirculation,

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Yasemin Khoury, M.Sc., 1991

Thesis: Ethanol Production from Glucose by Immobilized S.cerevisiae

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan 

  • Candan Tamerler, M.Sc., 1991

Thesis: A Small Purification Procedure for EcoRI Endonuclease,

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan          

  • Pemra Doruker, M.Sc., 1991

Thesis: Studies on Immobilized Ethanol Producing S.cerevisiae  ATTC 9763

Advisor: Prof. Dr. Betül Kırdar

Co-advisor: Prof. Dr. Z. İlsen Önsan